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Hi All, I my case, I need to copy fragment of a peptide, reverse the direction, set both peptides (original and reversed peptides) occupancy 0.5 and then I want to merge both peptides (into the original peptide), Coot won't allow me to do this and always change the peptide residue number in the copied fragment, I understand Coot won't allow merging two fragments with the same chain id and residue number with 1 occupancy without automatically renumbering residue, but in my case I think for the same chain id and residue number with half occupancy, it should be ok for Coot to merge without changing residue numbers. I do not know if it's right to put two merged half occupancy peptides (same sequence but reversed direction) with different chain id (Coot can merge it without problem) in the same area (density blob) as model (is this going to be a problem in refinement because Refmac will confused how two fragments are in the same blob?), I assume that every half occupancy fragment must have a partner with the same chain id and residue number that make the sum up to 1 occupancy (0.5+0.5=1) in any model. I'd appreciate any input on this. On Apr 28, 2016 2:32 AM, "Tristan Croll" <[log in to unmask]> wrote: > In my experience a text editor is often still the fastest way to do jobs > like this. A few hints: > > - make sure the peptide has a unique chain name. Many packages will get > very confused if you have two residues with the same chain and residue > number. > > - each chain should have a TER statement after it. Not all packages care > about this, but many do. > > - most packages will stop reading the PDB file when they hit an END > statement. Anything pasted in after that will be ignored. > > Hope this helps! > > Tristan > > > > Tristan Croll > Lecturer > Faculty of Health > School of Biomedical Sciences > Institute of Health and Biomedical Engineering > Queensland University of Technology > 60 Musk Ave > Kelvin Grove QLD 4059 Australia > +61 7 3138 6443 > > This email and its attachments (if any) contain confidential information > intended for use by the addressee and may be privileged. We do not waive > any confidentiality, privilege or copyright associated with the email or > the attachments. If you are not the intended addressee, you must not use, > transmit, disclose or copy the email or any attachments. If you receive > this email by mistake, please notify the sender immediately and delete the > original email. > > > > > On 28 Apr 2016, at 7:04 PM, chemocev marker <[log in to unmask]> > wrote: > > > > Hi > > I am trying to take the peptide-ligand from 1 x-ray structure into the > other x-ray structure. What I did is, I superimpose both structures and > save the ligand as a PDB file and copy the text coordinates and paste it > into the other X-ray structure, but it does not work. I know it can work > but I don't know how to do that. CCP4MG program does not allow me to save > the selected atom of 2 different PDB structure as one PDB file. If someone > have any idea how it can be done. > > > > best > > > > Jiri > > > > >